In humans, the Y chromosome spans 23 million base pairs (the building blocks of DNA) and represents approximately .38% of the total DNA in cells. The human Y chromosome contains only 78 genes, which in turn code for only 23 distinct proteins. This relationship is typical in that most species' Y chromosomes contain the fewest genes of any of the chromosomes.

Because the Y chromosome changes relatively slowly over time and is only passed along the direct male line, it may be used to trace paternal lineage. It also contains the lowest number of known genetic diseases (44 in total) related to humans.

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Each person normally has one pair of sex chromosomes in each cell. As a general rule, the Y chromosome is present in males, who have one X and one Y chromosome, while females have two X chromosomes. However there are exceptions where this is not the case, for details see Intersex. Many of the genes on the Y chromosome are involved in male sexual determination and development; the most important of them is the SRY gene, which seems to determine the sex in primates. (Other mammals may use a different gene.)

The human Y chromosome is unable to recombine with the X chromosome, except for small pieces on the ends, which comprise about 5% of the chromosome's length. About 56 (72 %) of the Y chromosome genes are in this area and as a result are common between the two sex chromosomes.

Many cold-blooded vertebrates have no sex chromosomes. If they have different sexes, sex is determined environmentally rather than genetically. For some of them, especially reptiles, sex depends on the incubation temperature, others are hermaphroditic.

X and Y chromosome diverged about 350 million years ago, when some reptile developed a gene which makes all its owners to be males. The chromosome with this gene became Y chromosome, and similar chromosome without it became X chromosome. So initially, X and Y chromosomes were almost the same. Genes which were beneficial for males and harmful for females (male genes) either moved into Y chromosome or developed in it. This was beneficial for both sexes.

However, recombination between X and Y chromosomes was harmful because it provided males without some male genes or females with some male genes. As a result, male genes assembled around the sex determining gene in order to make this less probable. Later, Y chromosome changed in such a way that the areas around the sex determining gene completely lost their ability to recombine with X chromosome.

With time, the larger and larger areas lost ability to recombine with the X chromosome. However, without recombination it is hard to get rid of harmful mutations. Therefore, harmful mutations increasingly damaged male genes until some stopped functioning and became genetic junk. The useless genes were then removed from Y chromosome.

As a result of this process, for humans 95% of Y chromosome is unable to recombine, and for some other animals, the degradation of Y chromosome is even more severe. For example, the Y chromosome in kangaroos contains only the SRY gene.

For humans and some other primates, the Y chromosome is able to "recombine" with itself (see below). This process, called gene conversion, may slow down the process of degradation.

After only an SRY (or other sex-determining) gene remains from the whole Y chromosome, there are following possibilities:

The gene is connected to X chromosome or some autosome, making it the new Y chromosome. The whole process starts again. This happened with two species of rodents (Ellobius tancrei and E. lutescens). In one species, both sexes have unpaired X chromosomes; in the other, both females and males have XX.

Part of some autosome is connected to both X and Y chromosome. This happened with one species of drosophila.

No vital genes reside only on the Y chromosome, since 50% of humans do not have Y chromosomes. The only well-defined human disease linked to a defect on the Y chromosome is defective testicular development (due to deletion or deleterious mutation of SRY. This results in sex reversal, so that a person with an XY karyotype has a female phenotype (i.e., is born a female). The lack of the second X results in her infertility.

However it is possible for an abnormal number (aneuploidy) of Y chromosomes to result in problems.

47,XYY syndrome is caused by the presence of a single extra copy of the Y chromosome in each of a male's cells. Males with 47,XYY syndrome have one X chromosome and two Y chromosomes, for a total of 47 chromosomes per cell. Researchers are not yet certain why an extra copy of the Y chromosome is associated with tall stature and learning problems in some boys and men. These effects are variable and often minimal or undetectable. When chromosome surveys were first done in the 1960s, it was reported that a higher than expected number of men in prisons were found to have an extra Y chromosome, so that for a while it was thought to predispose a boy to antisocial behavior (and was dubbed the "criminal karyotype"). Better populaton surveys have since demonstrated that the association was simply that boys and men with learning problems are more likely statistically to spend time in prison and that there is no other independent statistical association with extra Y. The "criminal karyotype" concept is inaccurate and obsolete.

Greater degrees of Y chromosome polysomy (e.g., XYYYY) are very rare. Rarely, males may have more than one extra copy of the Y chromosome in every cell (polysomy Y). The extra genetic material in these cases can lead to skeletal abnormalities, decreased IQ, and delayed development, but the features of these conditions are variable.

There are also problems that arise from having an incomplete Y chromosome: the usual karyotype in these cases is 46X, plus a fragment of Y. This usually results in defective testicular development, such that the infant may or may not have fully formed male genitalia internally or externally. The full range of ambiguity of structure may occur, expecially if mosaicism is present. When the Y fragment is minimal and nonfunctional, the child usually is a girl with the features of Turner syndrome but a risk of malignancy.

Klinefelter syndrome (47, XXY) is not an aneuploidy of the Y chromosome, but the extra X chromosome usually results in defective postnatal testicular function. This does not seem to be due to direct interference with expression of Y genes, and the mechanism is not fully understood.

Chromosomes have robust and accurate repair mechanisms. Over time random mistakes - mutations - occur throughout all chromosomes, and the existence of some high-accuracy repair mechanism is known to be necessary for the survival of the chromosome, and thus the species carrying the chromosome.

The primary repair mechanism is dependent upon the fact that all people receive two sets of each chromosome, one from their mother and one from their father. Over time damage occurs, yet at the same time, chromosome pairs swap damaged genes out and replace them with a copy of undamaged genes. Gene sequences on chromosomes are fixed by following the template on the homologous chromosome. This repair technique is called recombination, and repairs a great many errors. Errors not caught by this technique are weeded out over time through natural selection. Until recently such error-correcting mechanisms were known for all chromosomes in humans, with the exception of the Y chromosome.

While females have two X chromosomes, males only have one Y chromosome (and one X chromosome.) Without a homologous chromosome, the Y chromosome cannot utilize this repair mechanism. It is believed that when the sex chromosomes first evolved there was effectively only one type. Over time this diverged into the X and the Y chromosomes, each having roughly 1,000 protein-coding genes. As they diverged over time, the Y chromosome became significantly different from the X chromosome so that it could not swap genes. As such, without a then-extant repair mechanism, errors and deletions built up in the Y chromosome over time. Over time many of the Y chromosome's genes were damaged and then lost.

Since the Y chromosome did not have the same error-correcting machinery that all the other chromosomes have, this gave rise to widespread speculation that no error-correcting machinery existed within this chromosome at all. Without any such machinery, random errors in copying would logically and inevitably cause the destruction and disappearance of the Y chromosome in all animals. Indeed, over time it appears that the Y chromosome has indeed lost many of its original DNA material, and has become much smaller.

If this damage and loss were to continue unabated, this would lead to the disappearance of all males in any unisexual species in which males are the heterogametic sex, including humans. As a result, the only species that would survive in the long term would be those species that either evolved a female-only method of reproduction or employed a different sex determination mechanism. However, this line of reasoning was based on the sole assumption that lack of knowledge about Y chromosome repair meant that no possible repair mechanism could exist. This assumption was shown to be in serious error in 2003.

All other chromosomes occur in pairs. They preserve genetic integrity by exchanging information with matching genes on the homologous chromosome, a process called "crossing over." But the Y chromosome lacks that option, being the only chromosome that is unpaired. What was discovered in 2003 was that the Y chromosome exchanges genes between the two copies of repeated sequences that lie near to each other as mirror images. This phenomenon is called gene conversion. It is the non-reciprocal transfer of genetic information from one DNA molecule to another. It has been previously observed on a small scale over long evolutionary timescales between repeated sequences on the same chromosome, but not at the dramatic frequency apparently employed by the Y chromosome.

A research team, led by David C. Page, M.D., a Howard Hughes Medical Institute investigator at the Whitehead Institute for Biomedical Research in Cambridge, Mass.; Richard K. Wilson, Ph.D., director of the Genome Sequencing Center at Washington University School of Medicine in St. Louis; and Robert H. Waterston, M.D., Ph.D., formerly of Washington University's sequencing center and now at the University of Washington, Seattle, discovered that many of the sequences of chemical units -- called bases or base pairs -- that carry genetic information on the Y chromosome are arranged as palindromes.

In the case of the Y chromosomes, the palindromes are not "junk" DNA; these strings of bases contain functioning genes important for male fertility. Most of the sequence pairs are greater than 99.97 % identical. The extensive use of gene conversion appears to play a role in the ability of the Y chromosome to edit out genetic mistakes and maintain the integrity of the relatively few genes it carries.

Findings were confirmed by comparing similar regions of the Y chromosome in humans to the Y chromosomes of chimpanzees, bonobos (the pygmy chimpanzee) and gorillas. The comparison demonstrated that the same phenomenon of gene conversion appeared to be at work more than 5 million years ago, when humans and the non-human primates diverged from each other.

In human genetic genealogy (the application of genetics to traditional genealogy) use of the information contained in the Y chromosome is of particular interest since, unlike other genes, the Y chromosome is passed exclusively from father to sons.